[Jalview-discuss] export pictures of overview and via command-line

[Jim Procter]

Hi Timothée !
On 01/04/2010 12:24, Timothée Flutre wrote:
>
> 1) I would like to export the overview of the MSA as a picture. Is it 
> possible within Jalview, ie without taking a screencast? If yes, is it 
> possible to do via the command-line?
Currently no. The best you could do at the moment is generate a png and 
then use a command line tool (PNGtools for instance) to rescale the 
image. However, Albert and I have a plan to enable Jalview to more 
easily generate overview images.

> 2) Similarly, when I export a picture of the MSA via the command-line, 
> I run this command:
> $ java -Djava.ext.dirs=XXX/lib -cp XXX/jalview.jar jalview.bin.Jalview 
> -open myMsa.afa -png myPicture.png
> But is it possible to do so without having Jalview opening the window?
Sure. This is one thing we did think of :) The nodisplay argument stops 
the GUI starting:

java -Djava.ext.dirs=XXX/lib -cp XXX/jalview.jar jalview.bin.Jalview 
-nodisplay -open myMsa.afa -png myPicture.png

Jim.

ps. the -help argument will print all the command line arguments jalview 
understands.
pps. there is a bug in the current 2.4.0b2 version which causes sequence 
features not to be rendered on the PNG images when Jalview is run from 
the command line. This is fixed in the development version and will 
appear in the next release.

-- 
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J. B. Procter  (JALVIEW/ENFIN)  Barton Bioinformatics Research Group
Phone/Fax:+44(0)1382 388734/345764  http://www.compbio.dundee.ac.uk
The University of Dundee is a Scottish Registered Charity, No. SC015096.